ONTOPORTAL VIRTUAL APPLIANCE v2.5 IS NOW AVAILABLE

The NCBO Virtual Appliance has been updated to use NCBO's new v4.0 software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism. Please read below as much of the Appliance workflow has changed.

Virtual Appliance Basics

The NCBO Virtual Appliance is a copy of the NCBO software that you can run on your own Linux system. You have to install it following the instructions below, and upload your own ontologies (and/or copies of ours, if they are public).

The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system.

It is available as a VMWare Virtual Appliance OVF, as well as an Amazon Web Service AMI, and can be obtained by contacting us following the instructions under Getting Started below.

Please see below for how-to documentation for managing the software and running data population for Annotator.

You may also want to visit the Virtual Appliance FAQ for additional information on the Virtual Appliance, as well as the other pages in this category (bottom of the page).

Getting Started

VMWare Virtual Appliance

To obtain the VMWare Virtual Appliance, contact NCBO Support to initiate your request. You'll then be asked privately for your BioPortal account username, project goals, and reason for preferring the local installation.

You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer to this hostname as 'example'.

Change default passwords

Operating System

Username: root

Password: password is prompted on the first boot

BioPortal Admin User

Username: admin

Password: changeme

Amazon AWS AMI

For users who want to run their BioPortal instance on Amazon Web Services, an Amazon Machine Instance (AMI) is available on the BioOntology AWS Market Place. Please contact NCBO Support for more information.

Once the instance is running, enter the public DNS provided by Amazon into your browser to access BioPortal web interface. The default application administrator is 'admin' and the initial password is the Instance ID. You can also SSH to the machine using the username 'ec2-user' and your Amazon private key.

General Instruction

Virtual Appliance Web UI can be accessed at http://{ip_address_of_appliance}. You can get IP address of the Appliance by using the following command in the terminal 'ip addr show eth0'

System Requirements

The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.

Note: these requirements are for basic usage. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.